|
| Status |
Public on Jun 30, 2016 |
| Title |
Galactose, biological rep.1 |
| Sample type |
RNA |
| |
|
| Source name |
A.oryzae 1hr induction in galactose medium
|
| Organism |
Aspergillus oryzae RIB40 |
| Characteristics |
condition: galactose 1hr induction
|
| Treatment protocol |
Induction culture was performed at 100rpm for 1hr at 30°C with each three medium. Mycelium was harvested with Miracloth, washed with ice-chilled water twice and was dried with paper towel.
|
| Growth protocol |
Aspergillus oryzae RIB40 were pre-cultured in MM medium (1g glucose, 3g glutamate, 2 g NH4Cl, 1 g (NH4 )2SO4 , 0.5 g KCl, 1 g KH2 PO4 , 0.5 g MgSO47H2O, 0.02 g FeSO4 , 1.5 g L -methionine, in 1liter, pH6.5) at 100rpm for 24hr at 30°C. Mycelia was recovered by filtration using Miracloth (Calbiochem) and transferred to 100ml of each induction medium. MM and GM (MM+1% galactose without glucose), and SM (MM+1% sorbitol without glucose) medium were used. Induction culture was performed at 100rpm for 1hr at 30°C with each three medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelium was frozen by liquid N2 and ground. Total RNA was extracted with Isogen (Wako) according manufacturer’s instruction. Total RNA was purified for microarray analysis using an RNeasy minikit (Qiagen). RNA quality was determined using a BioAnalyzer 2100 system (Agilent Technology), and the quantity was determined using an Ultrospec 3300 pro spectrophotometer (Amersham Pharmacia Biotech).
|
| Label |
biotin
|
| Label protocol |
Fragmented biotin-labeled cRNA was prepared using a GeneChip one-cycle target labeling and control reagent kit (Affymetrix) according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
The fragmented cRNA was hybridized to an AoDNAChip. The A. oryzae GeneChip microarray (AoDNAChip; NCBI Gene Expression Omnibus [GEO] platform GPL16184) which was designed by Affymetrix was used for transcriptome analysis using probes of 13,765 ORFs set on this microarray.
|
| Scan protocol |
This GeneChip was washed, stained, and scanned using a GeneChip FS-450 fluidics station (fluidics protocol FS450_001) and a GeneChip 3000 scanner.
|
| Description |
Gene expression data from 1hr galacotse induction
|
| Data processing |
Scanned probe array images were converted into CEL files and normalized using the GCOS v.1.4 program (Affymetrix). Calculations of signal intensity and detection P values were also performed using GCOS v.1.4. The trimmed mean signal of the array was scaled to the target signal of 500 with the all probe sets scaling option. The detection call was used for detection of a particular transcript, with a detection P value of < 0.04 considered present (P), 0.04 ≦P < 0.06 considered marginal (M), and a P value of ≧ 0.06 considered absent (A). These calculation data were exported as CHP files. For microarray data analysis, CHP files were imported into GeneSpring v.7.3 (Agilent Technologies). Expression data were normalized per chip to the 50th percentile. Genes with statistically significant changes in transcript abundance were identified using a cutoff value of 2-fold and a Welch’s t test value of less than 5%.
|
| |
|
| Submission date |
Jan 05, 2016 |
| Last update date |
Jun 30, 2016 |
| Contact name |
Ken Oda |
| E-mail(s) |
[email protected]
|
| Phone |
+81-82-4200824
|
| Organization name |
National research institute of brewing
|
| Department |
Fundamental research division
|
| Lab |
Fungal biology lab.
|
| Street address |
3-7-1 Kagamiyama
|
| City |
Higashihiroshima |
| State/province |
Hiroshima |
| ZIP/Postal code |
739-0046 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16184 |
| Series (1) |
| GSE76534 |
Aspergillus oryzae gene expression with 1hr galactose, glucose, and sorbitol induction. |
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